tbuckley/cabot-search huggingface dataset:
Abstract 3829: Microenvironmental stiffness induces metabolic reprogramming in glioblastoma
Authors: Alireza Sohrabi, Austin Lefebvre, Michael Condro, Harley Kornblum, Michelle Digman, Stephanie Seidlits
Journal: Cancer Research (2022)

Abstract Glioblastoma (GBM) is the most common and lethal type of brain cancer with 5-year survival of &amp;lt;15%. The unique microenvironment of GBM is a key factor in tumor aggression. Similar to other solid tumors, GBM cells experience different biomechanical forces than do cells in healthy brain tissue. Here, we use atomic force microscopy to perform micro-compression mechanical analysis of xenografted GBM tumors. We show that tumors have a relatively stiff core (5-6 kPa Young’s modulus) and a softer edge (1-2 kPa Young’s modulus), yet all tumor tissue was stiffer than adjacent brain tissue (0.5-0.8 kPa Young’s modulus). To understand the functional implications of this biomechanical landscape, GBM spheroids were encapsulated in 3D culture matrices tuned to mimic the measured stiffnesses of a tumor regions and neighboring, non-cancerous tissue. These 3D matrices are fabricated from hyaluronic acid to promote GBM/matrix interaction through CD44 and RHAMM. RNA-sequencing analysis revealed overexpression of mitochondrial-encoded genes in stiff conditions, specifically genes encoding proteins involved in oxidation phosphorylation (OXPHOS), when compared to soft hydrogels. Using fluorescence-life time imaging microscopy to assess metabolic states at a single-cell level, we found that metabolism in GBM cells cultured in stiff matrices was dominated by OXPHOS while those in softer matrices was dominated by glycolysis (GLY). Furthermore, we show that this stiffness-induced shift towards OXPHOS in stiff matrices was associated with increased proliferation while the shift towards GLY in soft matrices was associated with increased migratory activity. Finally, inhibition of ezrin, an adaptor molecule linking the HA receptor CD44 to the actin cytoskeleton, eliminated the shift towards GLY induced in soft matrices, indicating that HA-CD44 interactions are necessary for these matrix-induced metabolic shifts. Citation Format: Alireza Sohrabi, Austin Lefebvre, Michael Condro, Harley Kornblum, Michelle Digman, Stephanie Seidlits. Microenvironmental stiffness induces metabolic reprogramming in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3829.
Abstract 2312: Efficacy of targeted osmotic lysis is increased by cell cycle inhibition in M Phase
Authors: Samantha Edenfield, Harry J. Gould, Dennis Paul
Journal: Cancer Research (2022)

Abstract Voltage-gated sodium channels (VGSCs) are upregulated in aggressive carcinomas, making these channels a target for novel clinical therapies. Targeted Osmotic Lysis (TOL) is a novel cancer therapy that combines pharmacologically blocking Na+,K+, ATPase (sodium pumps) while stimulating VGSCs with a pulsed electric field. The consequent increase in intracellular Na+ causes an osmotic lysis of the cells that overexpress VGSCs. Noncancerous cells, with fewer VGSCs do not lyse. We hypothesized that variability in efficacy of TOL is due to VGSC expression that varies across the cell cycle. We assessed cell surface expression of VGSCs and Na+,K+-ATPase during phases of the cell cycle in which there are single copies of DNA compared with phases in which DNA has doubled. For this, DNA was labeled with either propidium iodide or DAPI and VGSCs were labeled with a pan-specific VGSC antibody while Na+,K+-ATPases were labelled with a pan-specific Na+,K+-ATPase antibody in eight immortalized cancer and non-cancer cell lines. With flow cytometry we showed that VGSC expression doubled during phases of cell division (S-M phases) while Na+,K+-ATPase expression increased by 1.5-fold. To further elucidate the role of VGSCs and Na+,K+-ATPases throughout the cell cycle, S-Trityl-L-cysteine (STLC) was used to suspend the cell cycle in M phase. We hypothesized that treating cancer cells with TOL in the S-M phases would lead to increased cell death, compared to cells that were not suspended in M phase by STLC (G0-G1 phases). Cells were either treated with STLC or media without drug for 24 hours, then exposed to TOL treatment. The efficacy of the treatment was measured using a MTT assay revealing that cell death was greater in STLC-treated cells than control cells. By using cell cycle inhibitors, we may increase the efficacy of TOL for treating advanced carcinomas that overexpress VGSCs. Citation Format: Samantha Edenfield, Harry J. Gould, Dennis Paul. Efficacy of targeted osmotic lysis is increased by cell cycle inhibition in M Phase [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2312.
Abstract 799: HLTF and SHPRH in mismatch repair and cancer
Authors: Anna Kristin Miller, Guogen Mao, Christine Rahal, Christopher Putnam, Eva Goellner
Journal: Cancer Research (2022)

Abstract Colorectal cancer (CRC) is one of the leading causes of cancer deaths, with an increasing rate of CRC diagnosis in younger individuals. MMR is the DNA repair mechanism that repairs DNA mispairs and small insertions or deletions remaining after replication. MMR is also required for apoptosis after certain types of exogenous DNA damage that result in damage-associated mispairs. MMR defects are the underlying cause of Lynch syndrome, a familial cancer predisposition syndrome that increases susceptibility to multiple cancers, specifically colorectal cancer. MMR defects are also commonly found in sporadic colorectal cancers. Model systems such as Saccharomyces cerevisiae, Escherichia coli, and human cell lines have been used to study the MMR proteins and pathways. The basics of the MMR mechanism are fairly well understood; however, proteins associated with MMR are still being identified, and the roles of these proteins are largely unknown. We have identified the yeast protein Rad5 as an interactor with the yeast MMR proteins Msh2 and Mlh1. Rad5 is a helicase and an E3 ubiquitin ligase which is involved in post-replicative repair and damage tolerance. However, to date, Rad5 has no known role in MMR. We have determined that these interactions are conserved through evolution to human Rad5 homologs, HLTF and SHPRH. The Rad5 interactions with Mlh1 and Msh2 appear to be split between the human homologs with human Msh2 interacting with HLTF and human Mlh1 interacting with SHPRH. We have found that loss of SHPRH induces resistance to MMR-mediated apoptosis. Current experiments are in progress to determine the binding sites between these proteins. We are also investigating what functional impact the Rad5 homologs have on mutation rate and MMR-induced apoptosis and how the interactions affect the roles of MMR. Together this will allow for a deeper understanding of how accessory proteins may influence canonical and non-canonical MMR. Since MMR status is currently used to determine patient treatment, understanding how commonly mutated accessory factors interact is critical. Citation Format: Anna Kristin Miller, Guogen Mao, Christine Rahal, Christopher Putnam, Eva Goellner. HLTF and SHPRH in mismatch repair and cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 799.
Abstract 5997: The role of neutrophil extracellular trap-CCDC25-integrin linked kinase complex in pancreatic cancer progression and metastasis
Authors: Paul C. McDonald, Wells S. Brown, Zack Gerbec, Shannon Awrey, Joanna Karasinska, David Schaeffer, Daniel Renouf, Ben Stanger, Shoukat Dedhar
Journal: Cancer Research (2022)

Abstract Neutrophils and neutrophil extracellular traps (NETs) contribute to the hypoxic, immunosuppressive pancreatic ductal adenocarcinoma (PDAC) tumour microenvironment (TME) which promotes treatment resistance, increased invasion and metastasis. While recent studies have demonstrated a critical role of tumour cell CCDC25-ILK complex in promoting NET-DNA-induced tumour metastasis in breast cancer, here we have investigated the presence and function of NETosis-induced CCDC25-ILK signaling in the context of pancreatic cancer. We demonstrate that CCDC25 and ILK are expressed in human PDAC cell lines, patient-derived xenograft (PDX) cell lines and in cell lines derived from the KPCY genetic model of PDAC. Importantly, co-immunoprecipitation analyses showed that endogenous CCDC25 and ILK interact in PDAC cells, and the addition of neutrophil-derived NET-DNA resulted in a greater amount of ILK associated with CCDC25 and in increased wound-induced migration. Time-lapse imaging demonstrated a dramatic effect of inhibition of ILK activity on NET-DNA-induced migration by tumour cells in vitro. In vivo, co-localization of CCDC25 and ILK was observed in tumours and liver metastases from both the KPCY GEMM and the MIA PaCa-2 human PDAC xenograft models that were stained by multispectral immunofluorescence for these markers and analyzed by confocal microscopy. Similarly, both tumours and liver metastases showed the presence of infiltrating neutrophils and NETs as indicated by staining for myeloperoxidase and citrullinated histone H3. Collectively, these data identify the neutrophil extracellular trap-induced CCDC25-ILK interaction as an important contributor to PDAC progression and suggest the potential for targeting this axis to prevent NET-induced PDAC progression and metastasis. Citation Format: Paul C. McDonald, Wells S. Brown, Zack Gerbec, Shannon Awrey, Joanna Karasinska, David Schaeffer, Daniel Renouf, Ben Stanger, Shoukat Dedhar. The role of neutrophil extracellular trap-CCDC25-integrin linked kinase complex in pancreatic cancer progression and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5997.
Abstract 3048: CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data
Authors: Welles Robinson, Fiorella Schischlik, E. Michael Gertz, Joo S. Lee, Kaiyuan Zhu, S. Cenk Sahinalp, Rob Patro, Mark D. Leiserson, Alejandro A. Schaffer, Eytan Ruppin
Journal: Cancer Research (2022)

Abstract Despite recent reports of microbes living within tumor cells, the identification of intracellular microbes remains an open and important challenge. Here we introduce CSI-Microbes (computational identification of Cell type Specific Intracellular Microbes), a computational approach for the discovery of cell-type specific intracellular microbial taxa from single-cell RNA sequencing of host cells. It is first validated on two gold-standard datasets of human immune cells exposed to Salmonella. Next, CSI-Microbes is tested on Merkel cell and colorectal carcinoma where it identifies both reported and previously unknown tumor-specific intracellular microbes. Finally, CSI-Microbes is applied to analyze the intracellular microbiome of thirteen lung tumors where it identifies four tumors with bacterial taxa enriched in tumor cells and two tumors with bacterial taxa enriched in stroma or immune cells. Notably, the infected tumor cells down-regulate pathways associated with anti-microbial response and antigen processing and presentation, testifying to the functional significance of bacterial presence. Citation Format: Welles Robinson, Fiorella Schischlik, E. Michael Gertz, Joo S. Lee, Kaiyuan Zhu, S. Cenk Sahinalp, Rob Patro, Mark D. Leiserson, Alejandro A. Schaffer, Eytan Ruppin. CSI-Microbes: Identifying cell-type specific intracellular microbes from single-cell RNA-seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3048.
Abstract 1764: Development of an alphalex™-auristatin low pH targeting conjugate for the treatment of solid tumors
Authors: Sophia Gayle, Robert Aiello, Jane Bechtold, Patricia Bourassa, Johanna Csengery, Connor Hagen, Katia Howard, Kelli Jones, Lori Lopresti-Morrow, Robert Maguire, Timothy Paradis, Theresa Pasqualini, Joseph Tweed, Laurie Tylaska, Qing Zhang, Vishwas Paralkar
Journal: Cancer Research (2022)

Abstract Auristatins such as monomethyl auristatin E (MMAE) are a class of high potency microtubule targeting compounds that have an extremely narrow therapeutic window. Targeting potent auristatins to the tumor is the only feasible method of unlocking the clinical potential of such toxic molecules. While there are currently four marketed antibody-drug conjugates (ADCs) featuring auristatins, these ADCs face the same fundamental issues - tumor restriction by target antigen and the potential for off target release of payload. Alphalex࣪ is a tumor targeting technology consisting of a unique variant of a family of pH-Low Insertion Peptides (pHLIP®) that target acidic cell surfaces (references 1-2), a cleavable small molecule linker, and an anti-cancer agent warhead. Alphalex࣪ thereby allows for antigen independent targeting of the tumor and enables intracellular delivery of the warhead by leveraging the low pH microenvironment of the tumor, a universal feature common to all tumors due to the Warburg effect. Here we report the preclinical efficacy, safety, and antigen-independent tumor-targeting properties of alphalex࣪ conjugated to MMAE. We demonstrate the ability of alphalex࣪-MMAE to display potent in vitro and in vivo efficacy in colorectal, non-small cell lung, and prostate carcinoma cell lines. We further show that alphalex࣪-MMAE efficiently and safely delivers efficacious levels of MMAE selectively to tumor and demonstrates extreme plasma stability, with 0.02% warhead release over 24h in the rat. Based on the excellent preclinical safety and efficacy profile of alphalex࣪-MMAE, Cybrexa will move forward with the goal of initiating IND-enabling studies in 2022. References: 1. Wyatt LC, Lewis JS, Andreev OA, Reshetnyak YK, Engelman DM. Applications of pHLIP Technology for Cancer Imaging and Therapy. Trends Biotechnol. 2017 Jul;35(7):653-664. 2. Wyatt LC, Moshnikova A, Crawford T, Engelman DM, Andreev OA, Reshetnyak YK. Peptides of pHLIP family for targeted intracellular and extracellular delivery of cargo molecules to tumors. Proc Natl Acad Sci USA. 2018 Mar 20;115(12):E2811-E2818. Citation Format: Sophia Gayle, Robert Aiello, Jane Bechtold, Patricia Bourassa, Johanna Csengery, Connor Hagen, Katia Howard, Kelli Jones, Lori Lopresti-Morrow, Robert Maguire, Timothy Paradis, Theresa Pasqualini, Joseph Tweed, Laurie Tylaska, Qing Zhang, Vishwas Paralkar. Development of an alphalex™-auristatin low pH targeting conjugate for the treatment of solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1764.
Abstract 5019: Eliminating copy number alteration effects in the gene essentiality data from the Cancer Dependency Map project
Authors: Arkajyoti Bhattacharya, Carlos G. Urzúa-Traslaviña, Marcel A. T. M. van Vugt, Rudolf S. N. Fehrmann
Journal: Cancer Research (2022)

Abstract The Cancer Dependency Map project (DepMap) aims to identify cancer vulnerabilities through the in vitro study of genetic dependencies in cancer cell lines using CRISPR/Cas9 loss-of-function screens. Cas9-mediated DNA break formation induces toxic effects that are proportional with the number of cuts. Consequently, the DepMap data displays a ‘copy number alteration effect’ (CNA effect), in which sgRNAs targeting highly amplified regions of the genome produce depletion effects. Indeed, when sgRNAs target intergenic regions of amplified regions, the observed effects are comparable to the targeting of essential genes. Hence, correcting the CNA effect is crucial to reduce false positive (and increase true negative) co-dependencies between genes. Currently, the CERES methodology is used to correct for CNA effects. By applying a consensus-independent component analysis-based (consensus ICA) algorithm on gene essentiality data after CERES correction, we observed that many CNA effects are still present in the CERES-corrected data. Subsequently, we developed a methodology that outperforms CERES in removing the CNA effect. For example, we identified a set of genes mapping to chromosome 8q of sample ACH-000542 (ovarian adenocarcinoma cell line HEYA8 having amplification at chromosome 8q) having significantly lower essentiality levels compared to the rest of the genome. Whereas the CERES algorithm did not correct this effect of the chromosome 8q amplification, it was captured by consensus ICA in a consensus estimated source and was corrected by our novel methodology. After removing all CNA effects from gene essentiality data, we observed that 12.07% of co-dependency scores reported by CERES-corrected data decreased by 0.2 (on a range of -1 to 1), and 11.34% co-dependency scores increased by 0.2. In conclusion, consensus ICA-based methodology improves the correction of the CNA effect on gene essentiality data. Application of our improved method of CNA effect correction could reduce the number of false positive targets in validating biological hypotheses leading to novel therapeutic strategies in cancer. Citation Format: Arkajyoti Bhattacharya, Carlos G. Urzúa-Traslaviña, Marcel A. T. M. van Vugt, Rudolf S. N. Fehrmann. Eliminating copy number alteration effects in the gene essentiality data from the Cancer Dependency Map project [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5019.
Abstract 3538: A CTLA-4 targeted ETB for Treg depletion shows favorable preclinical efficacy and safety
Authors: Asis Sarkar, Rebecca Martin, Lauren R. Byrne, Caleigh Howard, Swati Khanna, Lilia A. Rabia, Diana Adhikari, Michaela M. Sousares, Alvaro Aldana, Garrett L. Robinson, Jay Zhao, Chris B. Moore, Aimee Iberg
Journal: Cancer Research (2022)

Abstract CTLA-4-targeted engineered toxin bodies (ETBs) are designed to deplete immune-suppressive regulatory T cells (Tregs) in the tumor microenvironment (TME) directly and in a manner independent of Fc-mediated effector functions, offering a unique approach to CTLA-4 targeted therapy that may show efficacy where blocking antibodies have failed. ETBs are large molecule proteins consisting of an antibody fragment genetically fused to a proprietary de-immunized (DI) form of the Shiga-like toxin-1 subunit A (SLTA). Once engaged to the specific cell surface target of interest, ETBs internalize, route to the cytosol, and permanently inactivate ribosomes through an irreversible enzymatic process. This results in cell death via apoptotic mechanisms. Here we describe the preclinical characterization of a candidate CTLA-4-targeted ETB. The candidate ETB kills gain-of-function model cell lines that express CTLA-4 at levels observed on primary human tumor Tregs. Notably, the potency of the candidate ETB is limited when CTLA-4 is expressed at low levels, thereby allowing a mechanism to spare CD8+ cytotoxic T lymphocytes (CTLs) and effector CD4+ T cells from targeted depletion. The candidate ETB binds CTLA-4 with high affinity utilizing a unique biparatopic binding domain. Using in vitro systems, we show that the candidate ETB can block CTLA-4:B7 interactions and repress Treg-mediated T-cell suppression. In a syngeneic mouse pharmacodynamic model, the candidate ETB depletes tumor-resident Tregs and increases the CD8:Treg ratio in the TME. A toxicological study in naive NHP demonstrate that the candidate ETB, which is cross-reactive to NHP, is well-tolerated at 450 mcg/kg (highest dose tested) administered intravenously once weekly for 4-weeks and does not significantly alter the CTLA-4 low/null peripheral T cell populations. Overall, the candidate ETB is a unique CTLA-4 targeting modality that is designed to deplete Tregs selectively and directly in the tumor, spare CD8+ CTLs, and represents an alternative treatment option to traditional blocking antibodies. Development activities are underway to support the upcoming IND application. Citation Format: Asis Sarkar, Rebecca Martin, Lauren R. Byrne, Caleigh Howard, Swati Khanna, Lilia A. Rabia, Diana Adhikari, Michaela M. Sousares, Alvaro Aldana, Garrett L. Robinson, Jay Zhao, Chris B. Moore, Aimee Iberg. A CTLA-4 targeted ETB for Treg depletion shows favorable preclinical efficacy and safety [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3538.
Abstract 1392: Development of a human T cell backbone flow cytometry panel enabling flexibility in reagent choice while minimizing panel design challenges
Authors: Mirko Corselli, Chad Sisouvanthong, Nihan Kara, Stephanie Widmann
Journal: Cancer Research (2022)

Abstract Advancements in flow cytometry have led to a comprehensive characterization of T cells. While many markers can be used for a detailed immunophenotypic or functional analysis, design of a large multicolor flow cytometry panel is still hampered by the selection of optimal fluorochrome combinations. For example, expansion of existing flow cytometry panels with new markers of interest can result is suboptimal resolution and, in some cases, the need to design a new panel, impacting cost and increasing time to insight. To minimize these challenges and to provide increased flexibility, we have developed a human T cell backbone panel strategically designed to be complemented with 5-8 drop-in markers of choice, depending on instrument configuration. The backbone panel contains five T cell markers (CD3, CD4, CD8, CD45RA, CCR7) conventionally used to identify different maturational states of CD4+ and CD8+ T cells (naïve, central memory, effector memory, effector memory RA). We will show how this backbone panel meets four fundamental requirements: i) clear resolution of major T cell subsets; ii) the fluorochromes used in the backbone panel have minimal resolution impact on the detectors allocated for drop-ins; iii) the fluorochromes assigned to drop-ins have minimal impact on the resolution of the backbone panel; iv) the fluorochromes assigned to drop-ins do not impact each other. We will provide examples of different drop-in combinations for the study of T cell and regulatory T cell biology. Performance of the backbone panel on different instruments will be shown to demonstrate assay consistency across platforms. The compatibility of the backbone panel with intracellular cytokine stain and transcription factor analysis will be further demonstrated. This pre-optimized backbone panel represents a unique tool for researchers who need to study different aspects of T cell biology and want to easily increase their assay capabilities, while minimizing panel design challenges and impact to population resolution. For Research Use Only. Not for use in diagnostic or therapeutic procedures. Citation Format: Mirko Corselli, Chad Sisouvanthong, Nihan Kara, Stephanie Widmann. Development of a human T cell backbone flow cytometry panel enabling flexibility in reagent choice while minimizing panel design challenges [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1392.
Oncology clinical trial disruption during the COVID-19 pandemic: a COVID-19 and cancer outcomes study
Authors: Z. Bakouny, C. Labaki, S. Bhalla, A.L. Schmidt, J.A. Steinharter, J. Cocco, D.A. Tremblay, M.M. Awad, A. Kessler, R.I. Haddad, M. Evans, F. Busser, M. Wotman, C.R. Curran, B.S. Zimmerman, G. Bouchard, T. Jun, P.V. Nuzzo, Q. Qin, L. Hirsch, J. Feld, K.M. Kelleher, D. Seidman, H. Huang, H.M. Anderson-Keightly, T. El Zarif, S. Abou Alaiwi, C. Champagne, T.D. Rosenbloom, P.S. Stewart, B.E. Johnson, Q. Trinh, S.M. Tolaney, M.D. Galsky, T.K. Choueiri, D.B. Doroshow
Journal: Annals of Oncology (2022)